Group 18: FINDING GENE PATTERNS IN BREAST CANCER DATA
Introduction:
Question: Which genes are differentially expressed in different subtypes of cancer?
General workflow
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General wokflow
EXPLORATORY ANALYSIS AND TIDY:
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Cleaning procedure
EXPLORATORY ANALYSIS AND TIDY:
DESEQ Analysis:
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DESEQ workflow
PCA Analysis:
Here is an analysis of PCA plots showing the scree and cumulative variance explained.
The high dimentionality required to explain 85% of the variability of the data shows that cancer analysis is a difficult task.
PCA Analysis:
- The highlighted genes for each PC might be linked to specific biological pathways or processes, as they represent the main drivers of variance for the data. -The PCA shows significant overlap between “TUMOR FREE” and “WITH TUMOR”, indicating no clear separation of cancer statuses.
Discussion: Biological insights
- We can see that the DE genes in the data affect most importantly X pathways
- This makes/not makes sense with the literature as 1,2,3